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Tracking issue for velvet-core release v0.2.0

This issue tracks the progress towards the v0.2.0 release of velvet-core on branch dev.

Add Boltzmann distribution temperature initialization
Specify Thermostat interface
Implement calculation of temperature as a property
Implement Nose-Hoover thermostat
Implement Berendsen thermostat
Conduct a simulation of Ar gas in the NVT ensemble
Add serde support for System and Potentials
Add benchmark test suite
Add documentation

Tracking issue for velvet-core release v0.5.0

This issue tracks the progress towards the v0.5.0 release of velvet-core on the branch master.

Add support for Coulomb potentials
- Implement the standard Coulomb potential
Enable optional f64 storage type as a cargo feature
Use neighbor lists to enhance performance of nonbonded interactions
Add the Buckingham pair potential
Conduct a simulation of MgO in the NVT ensemble
- Add as an example
- Validate against LAMMPS

Add all elements to Element enum

The Element enum currently supports only a minimal set of elements used in testing. All the naturally occurring elements from Hydrogen through Uranium should be implemented. The following snippet shows the existing implementation:

velvet/crates/velvet-core/src/system/elements.rs

Lines 5 to 83 in e4b3c46

 /// Every element on the periodic table. 

 #[derive(Clone, Copy, Debug, PartialEq, EnumString, Hash, Eq)] 

 pub enum Element { 

 /// Hydrogen 

 H, 

 /// Helium 

 He, 

 /// Boron 

 B, 

 /// Nitrogen 

 N, 

 /// Oxygen 

 O, 

 /// Fluorine 

 F, 

 /// Sodium 

 Na, 

 /// Magnesium 

 Mg, 

 /// Chlorine 

 Cl, 

 /// Argon 

 Ar, 

 /// Xenon 

 Xe, 

 } 

 impl Element { 

 /// Returns the atomic mass of the element in amu. 

 pub const fn mass(&self) -> Float { 

 match self { 

 Element::H => 1.008, 

 Element::He => 4.0026, 

 Element::B => 10.811, 

 Element::N => 14.0067, 

 Element::O => 15.999, 

 Element::F => 18.998, 

 Element::Na => 22.989, 

 Element::Mg => 24.305, 

 Element::Cl => 35.453, 

 Element::Ar => 39.948, 

 Element::Xe => 131.293, 

 } 

 } 

 /// Returns the electronic charge of the element as a multiple of electron charge. 

 pub const fn charge(&self) -> Float { 

 match self { 

 Element::H => 1.0, 

 Element::He => 0.0, 

 Element::B => 3.0, 

 Element::N => -3.0, 

 Element::O => -2.0, 

 Element::F => -1.0, 

 Element::Na => 1.0, 

 Element::Mg => 2.0, 

 Element::Cl => -1.0, 

 Element::Ar => 0.0, 

 Element::Xe => 0.0, 

 } 

 } 

 /// Returns the atomic number of the element. 

 pub const fn number(&self) -> u8 { 

 match self { 

 Element::H => 1, 

 Element::He => 2, 

 Element::B => 5, 

 Element::N => 7, 

 Element::O => 8, 

 Element::F => 9, 

 Element::Na => 11, 

 Element::Mg => 12, 

 Element::Cl => 17, 

 Element::Ar => 18, 

 Element::Xe => 54, 

 } 

 } 

 }

Tracking issue for velvet-core release v0.4.0

This issue tracks the progress towards the v0.4.0 release of velvet-core on the branch dev.

Tracking issue for velvet-core release v0.3.0

This issue tracks the progress towards the v0.3.0 release of velvet-core on the branch dev.

Tracking issue for velvet-core release v0.1.0

This issue tracks the progress towards the v0.1.0 release of velvet-core on branch dev.

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Tracking issue for velvet-core release v0.2.0

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Add all elements to Element enum

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	/// Every element on the periodic table.
	#[derive(Clone, Copy, Debug, PartialEq, EnumString, Hash, Eq)]
	pub enum Element {
	/// Hydrogen
	H,
	/// Helium
	He,
	/// Boron
	B,
	/// Nitrogen
	N,
	/// Oxygen
	O,
	/// Fluorine
	F,
	/// Sodium
	Na,
	/// Magnesium
	Mg,
	/// Chlorine
	Cl,
	/// Argon
	Ar,
	/// Xenon
	Xe,
	}

	impl Element {
	/// Returns the atomic mass of the element in amu.
	pub const fn mass(&self) -> Float {
	match self {
	Element::H => 1.008,
	Element::He => 4.0026,
	Element::B => 10.811,
	Element::N => 14.0067,
	Element::O => 15.999,
	Element::F => 18.998,
	Element::Na => 22.989,
	Element::Mg => 24.305,
	Element::Cl => 35.453,
	Element::Ar => 39.948,
	Element::Xe => 131.293,
	}
	}

	/// Returns the electronic charge of the element as a multiple of electron charge.
	pub const fn charge(&self) -> Float {
	match self {
	Element::H => 1.0,
	Element::He => 0.0,
	Element::B => 3.0,
	Element::N => -3.0,
	Element::O => -2.0,
	Element::F => -1.0,
	Element::Na => 1.0,
	Element::Mg => 2.0,
	Element::Cl => -1.0,
	Element::Ar => 0.0,
	Element::Xe => 0.0,
	}
	}

	/// Returns the atomic number of the element.
	pub const fn number(&self) -> u8 {
	match self {
	Element::H => 1,
	Element::He => 2,
	Element::B => 5,
	Element::N => 7,
	Element::O => 8,
	Element::F => 9,
	Element::Na => 11,
	Element::Mg => 12,
	Element::Cl => 17,
	Element::Ar => 18,
	Element::Xe => 54,
	}
	}
	}